Naruto - Zombie Apocalypse
by StrikeFromTheShadows
Summary: Konoha will stop at nothing to remain the most powerful and feared shinobi village. As the council orders research to be done on a method to create super ninjas, something dangerous is unleashed. Some things are better left undiscovered. Smart Naruto Slight AU Alternative Alternate Universe Power Strong Zombie Apocalypse Strength Intelligence Mini Harem Suspense Horror Tragedy
1. Chapter 1

**Naruto - Zombie Apocalypse**

**AN: I don't like having Naruto appear as a moron so on top of his ninja prowess, he will be a scientist in this fic. There will be a few ideas that are resident evil related but I will try to keep them minimal as I want this to be as original as it can.**

**Chapter 1: **_**IT HAS BEGUN!**_

Konoha was known as the most powerful of the five great shinobi nations. However, that wasn't good enough for them. The people of the leaf village _needed_ to be feared. As such, the council ordered research to be done for a new weapon. A secret weapon. It had begun. Three people had the most involvement in the _project_. Shikamaru Nara, Naruto Uzumaki, and Sasuke Uchiha. Granted, the council had only sent the Uchiha there to keep him happy, and he wasn't being much help. Luckily, there were tons of other scientists there to get things done, even if they aren't important enough to have notable names.

It had taken several months but the lead scientist Naruto Uzumaki could finally say that his team had succeeded. They had developed a serum that would allow them to create super ninjas. He was sure it would work even if it had only been tested on rats so far. The last thing left to was perform the final 'human test' and show granny Tsunade in the morning. With recent success on their mind, everyone went home for the night. Well, everyone except _Sasuke Uchiha_.

Naruto had slept good for the first time in years. As a result, he was running late. He left his apartment in a hurry and arrived at the lab the same time Shikamaru did, lazy bastard. Naruto opened the door and the two went inside. Things were unusually quiet. They went through the hallway and entered an empty lobby. Naruto turned to Shikamaru and asked the mutual unspoken question. "Where is everybody?" The genius Nara's eyes widened as groaning could be heard a short distance away. "Something's wrong. Naruto, send some shadow clones to go check that out." He nodded and formed an odd handsign. "Shadow clone jutsu!"

Most people would go rushing to see if that person was alright. However, Naruto and Shikamaru were certainly not most people. They were highly intelligent ninja that didn't want to take chances. A trait that would increase their chances for survival in the days to come. The shadow clones left the lobby and walked down another hallway towards the direction of the groan. A few seconds later, Naruto fell backward in surprise at the memories he received. He took on an almost 'Orochimaru-like skin tone' and looked up at Shikamaru. "The staff have turned _rabid_ and _cannibalistic._ We need to leave. Now!" He stumbled to his feet and quickly led Shikamaru back out the way they came.

The Uzumaki was a powerful ninja. In fact, he was one of the best ninja the leaf village had to offer. Shikamaru couldn't remember another time where Naruto looked so serious. It was for that reason that he wouldn't question Naruto. He wouldn't freak out like that needlessly or lie about such things. Two infected scientists came out of seemingly nowhere and rushed toward them. Naruto brought forth more shadow clones in order to witness firsthand what those _things_ could do.

One clone drew a kunai and stabbed the scientist in the chest. However, that didn't stop the infected staff member from pressing on. It bit the shadow clone's arm which in turn made it disperse. The remaining shadow clones attacked simultaneously to keep the infected occupied while Naruto and Shikamaru snuck past, running for the exit.

Two two left the building and Naruto faced the door. He went through handsigns in desperation. "Earth style: Earth wall!" A rocky pillar came out of the ground in front of the door, effectively blocking it. Shikamaru turned to Naruto with an obvious look of worry. "Naruto? Why didn't that thing die? Your shadow clone stabbed a fucking kunai through its chest!" The Uzumaki shook his head rapidly. "There's no time! We have to warn Granny Hokage. The earth wall should hold them back for now... Come on!" He shunshined away, leaving the Nara to grumble, "troublesome," and follow suit. If they would have stayed for a few more moments, they would have seen a chidori pierce the earth wall and the infected staff pouring out of the building.

_Hokage's Office_

Tsunade was sleeping in her office instead of working. It was probably safe to assume that her dream consisted of her actually winning whatever gambles she made and getting drunk. Those two things were high on her list of favorite things in life so getting woken up in the middle of such a dream would not make her happy. Consequently, only Naruto was hit over the head for his sudden disturbance. Why just him? Who knows?

Fortunately for Naruto, Tsunade saw a rare look of seriousness on his face and decided against a continued punishment. It was time for business. "Granny, something went wrong in the lab! We completed the development of the serum last night and went home. I slept in for once so I was late... So was Shikamaru but that's nothing new... Anyway, we went in and the whole staff... Someone must have used the serum on themselves and got infected and spread it to the others. It must not have been as 'complete' as we thought..."

The fifth Hokage looked toward Shikamaru as if expecting more information. The Nara sighed lazily and gave his report. "The workers bit Naruto's shadow clones so we can assume the infected pass the disease through broken skin. Once we got outside of the building, Naruto sealed the exit with an earth wall but who knows how long that will last."

Tsunade rubbed her temples. The stress was getting to her. She shook it off and went back into _'Hokage mode'. _"What do you think the best course of action-" Unfortunately, she was interrupted when Shizune burst in. "Lady Tsunade! There have been reports of crazy people biting villagers and Konoha-nins! The hospital can't keep up with the sheer number of victims!"

**AN: I will be needing a Beta reader for this. Pm me if interested. I'd prefer to have grammar edits or whatever done the same day which shouldn't be a problem as I don't make many mistakes with my typing. Plus, there should only be around 1k words per chapter.**

**This offer still stands until I remove the words. ;p**


	2. Chapter 2

**Naruto - Zombie Apocalypse**

_...Tsunade rubbed her temples. The stress was getting to her. She shook it off and went back into 'Hokage mode'. "What do you think the best course of action-" Unfortunately, she was interrupted when Shizune burst in. "Lady Tsunade! There have been reports of crazy people biting villagers and Konoha-nins! The hospital can't keep up with the sheer number of victims!"_

**Chapter 2: The Few That Remain**

_Hokage's Office_

Naruto's expression grew grim. "Multi shadow clone jutsu!" Mass copies of Naruto were brought into existence. There must have been at least a thousand. They darted off in different directions in order to fight off the infected. However, the original just stood there. He seemed to be deep in thought. There was an uneasy silence before he spoke. "There is something I must take care of. It may be our only chance." With that, Naruto was gone in a swirl of leaves.

_Streets of Konoha_

In the streets of Konoha, small groups of the remaining ninja fought together against the infected. It was a losing battle so once the mass amounts of shadow clones made an appearance, people were grateful. The clones began repeating an order over and over to ensure everyone left could hear it as they moved in to engage the infected. "Head to the forest of death! We will handle things here."

Slowly but surely, the survivors were escorted away as the shadow clones took over. The loss in strength made things difficult for the clones but they made up for the disadvantage with numbers. Unfortunately, the numbers didn't help much because the infected couldn't seem to be killed. "Why wont they die," one clone howled in frustration as he jammed yet another kunai into an infected Hyuuga's throat.

Eventually, the clones came across an isolated survivor. Itachi Uchiha. He was currently fighting against an infected Akimichi. It seemed ninja that were turned still had some control over their abilities. Good thing the Uchiha clan had all but died out. Those inbred fools produced less quality shinobi over time. Otherwise, they could have posed a huge threat as zombies.

The shadow clones rushed to assist but they quickly learned that their help wasn't needed. Itachi drew a katana and split the Akimichi's skull in half horizontally. The large man fell to the ground and was still. Itachi truly was a genius. He had discovered an effective way to kill those things. He nodded at the clones and dispersed into a flock of crows, which obviously meant that he had heard the instructions and was long gone.

There was a new arrival. An unexpected one. The infected Sasuke Uchiha. However, something was different about him. "Naruto." That came as a surprise. The infected were mindless. None of them were able to speak before. "I can feel my consciousness fading. I wont be able to fight this much longer. As it is, I can't control my body... I used the serum on myself to gain power but it backfired. I lost control of my body and infected the staff and the village... Please.. Kill me now. Before I become one of those _things._"

That was a tough thing for someone to ask for and something Naruto would never do. He could never even consider killing his best friend. A shadow clone shook his head and felt tears running down his face. "Sasuke, I can't do that! No. I'm going to find a way to save you! I will bring you back, I promise!" That way the last thing Sasuke heard. The light faded from his eyes and was replaced with a empty stare, just like all the others. For now, the remaining shadow clones would fight on. Their new mission would be to buy as much time as possible.

_Naruto's apartment_

Since Naruto was the lead scientist on the project and very dedicated, he often brought 'work' home with him. It just so happened that he had extra samples of the 'super ninja' serum in his apartment. What he was about to do was almost certainly suicide but it was also one of the only available options left. Perhaps the Kyuubi would prove itself useful for once and cleanse his system. Naruto pulled out the syringe and injected himself with the serum. There was intense pain and then darkness.

_Forest of Death_

All of the survivors had been gathered in front of the forest of death. People were there that didn't even receive instructions from Naruto. Tsunade must have ordered them to show up there which would most likely be thanks to Shikamaru's intelligent advice. Logically, it's a smart move because there aren't usually anybody in or near the forest of death so there's a minimal chance the infected would be drawn there for a while.

The survivors consisted of Yamato, Shizune, Might Gai, Shikaku, Ino, Lee, Kurenai, Tsunade, Sai, Kakashi, Shikamaru, Itachi, Kiba, Inoichi, Anko, Neji, and a cat mask ANBU. There wasn't a single person that was content with this situation. Even Sai looked like there were people he was missing. The group sat in silence for a while until Naruto finally made an appearance.

It was a relief to have Naruto there but something was different about him. Nobody said anything, they just stared. There was an eerie breeze of wind and Naruto broke the silence with a tone that commanded authority. "As some of you may know, several months ago the council ordered research to be done in order to create 'super ninjas'. I was part of that development team. We were close but something went wrong... Sasuke used the serum on himself and became rabid and cannibalistic. He infected the entire staff which eventually spread to the majority of the village. Konoha is lost... We must go to Suna. I am certain that Gaara will take us in."

He was met with mixed reactions. Some people didn't care what happened next, some found his words 'logical', and others had different opinions... The rash and hot headed Kiba was a good example. "We have to fight those things! This is our village, we can't just abandon it!" However, not everyone agreed with him. Shikamaru let out an annoyed noise and gave a logical response. "Look at how few of us remain... We can't fight them anymore... Lady Hokage, what will you have us do?"

All eyes were on Tsunade. She did not respond right away and instead began to massage her temples. Moments later groaning was heard in the distance and the tired Kage spoke. "It appears the decision has been made for us."

**AN: If anyone wants to **_**suggest**_** additional survivors, feel free to do so.**

**Jiraiya is away from the village, if anyone cares.**


	3. Chapter 3

**Naruto - Zombie Apocalypse**

_...All eyes were on Tsunade. She did not respond right away and instead began to massage her temples. Moments later groaning was heard in the distance and the tired Kage spoke. "It appears the decision has been made for us."_

**AN: I've been having a hard time writing this; I apologize. On top of my writer's block, I've been really busy. However, I should acknowledge the fact that I've been updating my other fics and neglecting this one. Not what I intended.**

**Chapter 3: A Trip To Suna**

_Flashback_

_ The zombies were closing in on the small group &amp; a combined ninjutsu attack made an opening for an escape. Naruto sent a few hundred clones back into the village to run interference and look for any additional survivors. They ended up finding Sakura, the Hyuuga sisters and the Konohamaru squad. It wasn't much, but every single person counted._

_End Flashback_

The remaining Leaf-nin leapt from tree to tree as they pushed for Suna. Almost three days had past since their departure from Konoha. Everyone was tired but unable to get much sleep because of the new horrors they had faced recently. The world as they knew it had changed, and not for the better. From here, things could only get worse.

Once they arrived in Suna, it was obvious that the hidden sand village had heard something of the situation. The gate guards were on high alert and spotted the group immediately. "Escort the visitors to the Kazekage, quickly! He has been expecting them." They had obviously had some idea on what had happened in Konoha. Scouts were always useful.

The group was ushered into Gaara's chambers where the young leader looked on with a rare look of worry on his normally stoic face. Joining him were Kankuro and Temari. Tsunade confirmed &amp; expanded the intel that Suna possessed. So far, the sand village was untouched by the undead &amp; was well protected by natural defenses. Gaara was not happy that the leaf had been the cause of everything but his relationship with Naruto made him willing to overlook that detail.

Most of the minor villages were likely to fall within the next few days or so. They did not have the man power to defend effectively against so many enemies. On top of that, only the major villages had decent natural protection, with a few exceptions. The leaf was the origin of the problem and the undead attacked from within so it didn't matter either way for them.

"We aren't in danger at the moment so we should use this time to gather supplies and strengthen our defenses. I have already recalled all shinobi that were out of the village. Everyone is accounted for. In addition, we must increase our strength so train hard, I want everyone in top condition. Kankuro. Temari. Relay my orders to the village."

With a nod, the two left to complete their tasks. Gaara was not in command of the remnants of the leaf so to them, his speech was more of a suggestion than anything else. Nonetheless, they agreed with him and had planned on training anyway. Besides, they were living inside his walls. The least they could do was show him some respect.

_Three Day Timeskip_

There was an underground cavern where the hidden sand got their water a short way from the village. Multiple trips were made in an effort to gather as much water as possible. Suna mostly imported their goods but that wouldn't be possible anymore. Luckily, they did grow some exotic things in their desert. It would be an early harvest this year.

Despite the despair everyone was feeling, they pushed themselves with training much harder than ever before. Naruto trained in secret. As a ninja, it was understandable to keep your strength and ability hidden but Naruto wasn't one to enjoy solitude. It was strange, _almost as if he had something to hide._

_Present Time_

The group had received word from scouts that the only surviving minor villages were the hidden waterfall, the hidden rain, and the hidden grass which was about to fall. However, there was another village. The hidden sound. It was essentially an extension of the leaf village. Orochimaru conducted research experiments there and built up a second military force in secret, by order of the council. It consisted of a series of underground bunkers.

Itachi was a man that paid attention to detail. He was not one to forget things but with everything that was going on, it was to be expected. Only a select few knew of the hidden sound's existence and the Hokage was a drunken fool. She could not be asked to remember anything of such importance. "lady Tsunade, might I suggest we call upon our forces in reserve?" Her eyes widened in realization. Things could get a lot better.

The ninja were getting restless and antsy. A few of the older ninja were bitter that the leaf had created this problem but the majority still held their allies in high regard. A jounin that hoped to achieve glory from victory against the undead spoke up. "Lord Kazekage, the ninja world suffers heavy losses. Will we do nothing to stop this madness?"

"Right now, we have other jobs that take priority. We have limited time to prepare and we would do well not to waste our resources and manpower so early on," the leader responded. The man grumbled in discontent, unable to come up with a counterargument.

**AN: I need suggestions on where to take this story so any ideas would be helpful. Even if they wouldn't be used right away. Please send me whatever you can think up because to be honest, I haven't planned this out at all. ;p**

**Read &amp; Review.**


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